Abstract
BackgroundTongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties.ResultsA total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition.ConclusionsTongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-014-0022-5) contains supplementary material, which is available to authorized users.
Highlights
Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties
Tongil rice (IR667-98-1-2) is the first semi-dwarf variety obtained by a three-way cross of indica/japonica varieties as part of a collaborative research project between the International Rice Research Institute (IRRI) and the government of South Korea (Figure 1)
We detected a total of 2,149,991 Single nucleotide polymorphism (SNP) between Tongil and Nipponbare sequences (Additional file 2: Table S2)
Summary
Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Demands on the nutritional and industrial functionality of rice are increasing, especially to improve human health and quality of life, improving the yield potential of rice is still a major challenge for rice breeders, who must address the rapid growth of the world may enrich allelic variation and facilitate hybrid vigor by creating new genetic recombinations (Cheng et al 2007) In spite of these advantages, the introduction of desirable indica traits into the japonica variety has not been successful due to reproductive barriers and the incorporation of undesirable characteristics, such as low eating quality for people who prefer the taste of japonica rice (Chung and Heu 1991). The genome characterization and structure of Tongil rice have never been analyzed
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